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Limits and file formats
Check which files Plasmole reads and writes, and the size and batch limits for each tool.
This page lists file formats, size limits and batch caps in one place. Plan allowances are on Plans and limits.
Import formats
Open the Library, click Import, and use the File tab.
| Kind | File extensions |
|---|---|
| GenBank | .gb, .gbk, .genbank |
| FASTA | .fasta, .fa, .fas, .fna |
| SnapGene | .dna |
| SBOL | .sbol, .xml |
| ApE | .ape |
| EMBL | .embl, .em |
| GFF | .gff, .gff3 |
| Sanger traces and reads | .ab1, .abi, .fastq, .fq |
| Archives | .zip |
| Documents and tables | .pdf, .docx, .doc, .xlsx, .xls, .csv, .tsv, .txt, .md |
The other tabs are Addgene (by plasmid ID), NCBI (by accession), Benchling and BLAST query. The Benchling tab reads a CSV or TSV file. It updates details on plasmids you already have and imports no sequences.
Export formats
| What | Formats |
|---|---|
| One plasmid | GenBank (.gb), FASTA (.fasta), SBOL (.xml), ApE (.ape) |
| Many plasmids | One ZIP in any of the four formats above |
| Map image | SVG, PDF, or PNG at 150 to 1200 DPI |
| Notebook entry | PDF, Word, Markdown |
Plasmole reads SnapGene .dna files but does not write them. Export GenBank to open a plasmid in SnapGene. See Export your data and get help.
File size limits
| What | Limit |
|---|---|
| SnapGene or SBOL file | 25 MB |
| Sanger trace or FASTQ file | 10 MB each |
| Benchling metadata CSV | 10 MB |
File imported as a new entry (.docx, .md, .xlsx, .xls, .csv) |
10 MB |
| Image in an entry | 10 MB |
| File attached to an entry | 50 MB |
| BLAST query file | 256 KB |
| Records added to an AI message | 10 items, 5 MB each, 20 MB total |
| Images in an exported entry PDF | 8 MB each, 32 MB total |
Batch and size caps
| Tool | Cap |
|---|---|
| Primer design, batch | 96 targets |
| Primer design, pairs shown for one target | Up to 10 |
| Primer design, candidate pairs per batch target | 5 by default, up to 20 |
| CRISPR guides, one target | 50 guides |
| CRISPR guides, batch | 96 targets, 50,000 bp each, 500,000 bp in total |
| CRISPR guides per batch target | 4 by default, up to 20 |
| CRISPR guide library import | 1 MB, 10,000 rows, guides 17 to 25 nt |
| Sanger verification, batch | 200 traces |
| Multiple sequence alignment | 2 to 50 sequences |
| Pairwise alignment | 100,000 bp per sequence |
| BLAST query | 10 to 50,000 bases |
| BLAST hits | 10 by default, up to 50 |
| Library Export as ZIP | 100 plasmids per ZIP; larger selections download as several ZIPs |
| Library Align against reference | 500 plasmids |
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